bio-spatial-transcriptomics-spatial-visualization

name	bio-spatial-transcriptomics-spatial-visualization
description	Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.
tool_type	python
primary_tool	squidpy

Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, scanpy 1.10+, squidpy 1.3+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Spatial Visualization

"Plot gene expression on my tissue section" -> Overlay gene expression, cluster assignments, or continuous scores on spatial coordinates with optional histology image background.

• Python: squidpy.pl.spatial_scatter(adata, color='gene'), scanpy.pl.spatial(adata, color='leiden')

Create visualizations for spatial transcriptomics data.

Required Imports

import squidpy as sq
import scanpy as sc
import matplotlib.pyplot as plt

Basic Spatial Plot

Goal: Create a spatial scatter plot with spots colored by a variable of interest.

Approach: Use Squidpy's spatial_scatter to overlay expression or metadata values on tissue coordinates.

# Plot spots colored by a variable
sq.pl.spatial_scatter(adata, color='total_counts', size=1.3)

# Multiple variables
sq.pl.spatial_scatter(adata, color=['total_counts', 'n_genes_by_counts'], ncols=2)

Plot with Scanpy

# Scanpy's spatial plot
sc.pl.spatial(adata, color='leiden', spot_size=1.5)

# Multiple genes
sc.pl.spatial(adata, color=['GENE1', 'GENE2', 'GENE3'], ncols=3)

Show Tissue Image

# Plot with tissue background
sc.pl.spatial(adata, color='leiden', img_key='hires', alpha_img=0.5)

# Without tissue
sc.pl.spatial(adata, color='leiden', img_key=None)

Customize Appearance

# Adjust spot size and colors
sc.pl.spatial(
    adata,
    color='leiden',
    spot_size=1.5,
    palette='tab20',
    title='Cluster assignments',
    frameon=False,
)

Gene Expression on Tissue

Goal: Visualize gene expression patterns overlaid on tissue spatial coordinates.

Approach: Plot individual or multiple genes using Scanpy's spatial plot with configurable colormaps and value ranges.

# Single gene
sc.pl.spatial(adata, color='CD3D', cmap='viridis', vmin=0, vmax='p99')

# Multiple genes side by side
genes = ['CD3D', 'MS4A1', 'CD14', 'NKG7']
sc.pl.spatial(adata, color=genes, ncols=2, cmap='Reds', vmin=0)

Expression with Colorbar Control

fig, axes = plt.subplots(1, 2, figsize=(12, 5))

for ax, gene in zip(axes, ['GENE1', 'GENE2']):
    sc.pl.spatial(adata, color=gene, ax=ax, show=False, vmin=0, vmax=5, cmap='viridis')
    ax.set_title(gene)

plt.tight_layout()
plt.savefig('gene_expression.png', dpi=300)

Compare Conditions/Samples

# Split by sample
sc.pl.spatial(adata, color='leiden', groups=['sample1', 'sample2'], ncols=2)

# Or manually
samples = adata.obs['sample'].unique()
fig, axes = plt.subplots(1, len(samples), figsize=(5*len(samples), 5))

for ax, sample in zip(axes, samples):
    adata_sub = adata[adata.obs['sample'] == sample]
    sc.pl.spatial(adata_sub, color='leiden', ax=ax, show=False, title=sample)

plt.tight_layout()

Overlay Annotations

# Plot with custom annotations
fig, ax = plt.subplots(figsize=(8, 8))
sc.pl.spatial(adata, color='leiden', ax=ax, show=False)

# Add text annotations
for cluster in adata.obs['leiden'].unique():
    mask = adata.obs['leiden'] == cluster
    coords = adata.obsm['spatial'][mask].mean(axis=0)
    ax.annotate(f'C{cluster}', coords, fontsize=12, ha='center')

plt.savefig('annotated.png', dpi=300)

Co-expression Plot

Goal: Visualize co-localization of two genes using dual-channel RGB encoding.

Approach: Normalize expression of each gene to [0,1], assign to red and green channels, and render as a scatter plot.

# Visualize co-expression of two genes
import numpy as np

gene1, gene2 = 'CD3D', 'CD8A'
expr1 = adata[:, gene1].X.toarray().flatten()
expr2 = adata[:, gene2].X.toarray().flatten()

# Create RGB image (red=gene1, green=gene2)
from matplotlib.colors import Normalize
norm = Normalize(vmin=0, vmax=np.percentile(np.concatenate([expr1, expr2]), 99))
colors = np.zeros((adata.n_obs, 3))
colors[:, 0] = norm(expr1)  # Red channel
colors[:, 1] = norm(expr2)  # Green channel

fig, ax = plt.subplots(figsize=(8, 8))
coords = adata.obsm['spatial']
ax.scatter(coords[:, 0], coords[:, 1], c=colors, s=10)
ax.set_aspect('equal')
ax.set_title(f'{gene1} (red) + {gene2} (green)')
plt.savefig('coexpression.png', dpi=300)

Visualize Spatial Statistics

# Plot Moran's I results
sq.pl.spatial_scatter(adata, color='GENE1', size=1.3)

# Plot neighborhood enrichment
sq.pl.nhood_enrichment(adata, cluster_key='leiden')

# Plot co-occurrence
sq.pl.co_occurrence(adata, cluster_key='leiden')

Interactive Visualization with Napari

Goal: Explore spatial data interactively with zoomable tissue images and spot overlays.

Approach: Load tissue images and spot coordinates into napari layers for pan-and-zoom exploration.

import napari

# Create viewer
viewer = napari.Viewer()

# Add tissue image
library_id = list(adata.uns['spatial'].keys())[0]
img = adata.uns['spatial'][library_id]['images']['hires']
viewer.add_image(img, name='tissue')

# Add spots
coords = adata.obsm['spatial']
scalef = adata.uns['spatial'][library_id]['scalefactors']['tissue_hires_scalef']
viewer.add_points(coords * scalef, size=10, name='spots')

napari.run()

Save Publication-Quality Figures

Goal: Export high-resolution spatial plots suitable for publication.

Approach: Configure frameless spatial plots with appropriate DPI and save as both PDF and PNG.

import matplotlib.pyplot as plt

fig, ax = plt.subplots(figsize=(8, 8))
sc.pl.spatial(
    adata,
    color='leiden',
    ax=ax,
    show=False,
    frameon=False,
    title='',
    legend_loc='right margin',
)
plt.savefig('figure.pdf', dpi=300, bbox_inches='tight')
plt.savefig('figure.png', dpi=300, bbox_inches='tight')

Multi-Panel Figure

Goal: Assemble a composite figure combining spatial plots, gene expression, UMAP, and violin plots.

Approach: Create a 2x3 subplot grid with different visualization types for comprehensive data overview.

fig = plt.figure(figsize=(15, 10))

# Tissue with clusters
ax1 = fig.add_subplot(2, 3, 1)
sc.pl.spatial(adata, color='leiden', ax=ax1, show=False, title='Clusters')

# Gene 1
ax2 = fig.add_subplot(2, 3, 2)
sc.pl.spatial(adata, color='CD3D', ax=ax2, show=False, title='CD3D', cmap='Reds')

# Gene 2
ax3 = fig.add_subplot(2, 3, 3)
sc.pl.spatial(adata, color='MS4A1', ax=ax3, show=False, title='MS4A1', cmap='Blues')

# QC metrics
ax4 = fig.add_subplot(2, 3, 4)
sc.pl.spatial(adata, color='total_counts', ax=ax4, show=False, title='Total counts')

# UMAP
ax5 = fig.add_subplot(2, 3, 5)
sc.pl.umap(adata, color='leiden', ax=ax5, show=False, title='UMAP')

# Violin plot
ax6 = fig.add_subplot(2, 3, 6)
sc.pl.violin(adata, ['CD3D', 'MS4A1'], groupby='leiden', ax=ax6, show=False)

plt.tight_layout()
plt.savefig('multi_panel.png', dpi=300)

Crop and Zoom

# Zoom into a region
x_min, x_max = 2000, 4000
y_min, y_max = 2000, 4000

fig, ax = plt.subplots(figsize=(8, 8))
sc.pl.spatial(adata, color='leiden', ax=ax, show=False)
ax.set_xlim(x_min, x_max)
ax.set_ylim(y_max, y_min)  # Note: y is inverted in images
plt.savefig('zoomed.png', dpi=300)

Related Skills

• spatial-data-io - Load spatial data
• spatial-statistics - Compute statistics to visualize
• single-cell/clustering - Generate cluster labels